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We also found that the relatedness of epitopes to the structural flexibility of a target protein surface is dependent on the secondary structure elements of paratopes. Monobody and repebody, whose binding sites are composed of β-strands, distinctively prefer to bind to a relatively more rigid region of a target protein. check details These observations enabled us to develop a simple epitope prediction method which shows a comparable performance to the commonly used ones.The challenge of assigning the absolute stereochemical configuration to a chiral compound can be overcome via accurate ab initio predictions of optical rotation, a sensitive molecular property that is further complicated by solvent effects. The solvent's "chiral imprint"-the transfer of the chirality from the solute to the surrounding achiral solvent-is explored here using conformational averaging and time-dependent density-functional theory. These complex solvent effects are taken into account via simple averaging over a molecular dynamics trajectory together with the explicit quantum mechanical consideration of the solvent molecules within the solute's cybotactic region and implicit modeling of the bulk solvent. We consider several axes along which the system's optical rotation varies, including the sampling of the dynamical trajectory, the quality of the one-electron basis set, and the use of continuum solvent models to account for bulk effects.Polymannuronate (PM) is an acidic polysaccharide prepared from alginate, contained in edible brown seaweeds. An unsaturated mannuronate oligosaccharide (MOS) is an enzymatically depolymerized oligosaccharide prepared from PM. The effects of MOS on attenuating tauopathy were studied in HEK293/Tau cells and primary triple transgenic (3×Tg) neurons. MOS inhibited heparin-induced aggregation of the Tau-K18 oligomer and suppressed the levels of phosphorylated Tau protein. MOS treatment reduced the activity of glycogen synthase kinase-3β (GSK-3β) by decreasing its phosphorylation levels on the sites of Y216 and increasing phosphorylation levels on the sites of S9. MOS treatment increased the ratio of LC3-II/LC3-I levels and reduced the expression of p62, indicating an increase in autophagy. Finally, MOS-induced decrease in Tau protein expression was attenuated by the addition of an autophagy inhibitor, confirming the involvement of autophagy. These data support MOS as a promising functional food or potential pharmaceutics for attenuating Tau protein-related disease.Many optoelectronic devices based on organic materials require rapid and long-range singlet exciton transport. Key factors controlling exciton transport include material structure, exciton-phonon coupling and electronic state symmetry. Here, we employ femtosecond transient absorption microscopy to study the influence of these parameters on exciton transport in one-dimensional conjugated polymers. We find that excitons with 21Ag- symmetry and a planar backbone exhibit a significantly higher diffusion coefficient (34 ± 10 cm2 s-1) compared to excitons with 11Bu+ symmetry (7 ± 6 cm2 s-1) with a twisted backbone. We also find that exciton transport in the 21Ag- state occurs without exciton-exciton annihilation. Both 21Ag- and 11Bu+ states are found to exhibit subdiffusive behavior. Ab initio GW-BSE calculations reveal that this is due to the comparable strengths of the exciton-phonon interaction and exciton coupling. Our results demonstrate the link between electronic state symmetry, backbone torsion and phonons in exciton transport in π-conjugated polymers.Periodic pattern formation beyond conventional precipitation reactions of electrolytes is of greater importance for gaining insights into the driving forces behind spontaneous spatiotemporal pattern formation in living matter. The Liesegang phenomenon is considered to be one of the important models for understanding well-defined periodic patterns. In this study, we have used biomolecule-derived photoluminescent carbon nanodots as reducing agents that were embedded in thin polymer films. The poor water content of polyvinyl alcohol/polyvinyl pyrrolidone films has been found to dictate the temporal scale of reaction-diffusion kinetics. Moreover, the precursors for the synthesis of nanodots have been varied to decipher the role of thiol groups present in glutathione in micron-spaced pattern formation of silver nanoparticles. A method to develop periodic patterns of plasmonic silver nanoparticles is of significant interest from technological aspects. Moreover, the formation of a micron-spaced pattern has been rationed by invoking a lowered nucleation threshold in terms of slow reaction-controlled aggregation. We expect that such an understanding of the chemical reaction-based pattern formation will help in resolving the formation of artistic spatiotemporal patterns in nature.Boronic acid-catalyzed regioselective Koenigs-Knorr-type glycosylation is presented. The reaction of an unprotected or partially protected glycosyl acceptor with a glycosyl halide donor in the presence of silver oxide and a low catalytic amount of imidazole-containing boronic acid was found to proceed smoothly, which enables construction of a 1,2-trans glycosidic linkage with high regioselectivities. This is the first example of the use of a boronic acid catalyst to initiate regioselective glycosylation via the activation of cis-vicinal diols in glycosyl acceptors.Electron paramagnetic resonance (EPR) spectroscopy is an established technique to site-specifically monitor conformational changes of spin-labeled biomolecules. Emerging in-cell EPR approaches aiming to address spin-labeled proteins in their native environment still struggle to reach a broad applicability and to target physiologically relevant protein concentrations. Here, we present a comparative in vitro and in-cell double electron-electron resonance (DEER) study demonstrating that nanomolar protein concentrations are at reach to measure distances up to 4.5 nm between protein sites carrying commercial gadolinium spin labels.The aim of this study was to improve our knowledge on the chemical markers of Cognac aromas. We report results concerning the distribution and sensorial impact of 3-methyl-2,4-nonanedione (MND), a well-known compound in aged red wine, reminiscent of anise or "dried fruit", according to its concentration. We assayed first this diketone (solid-phase microextraction (SPME)-gas chromatography (GC)/mass spectrometry (MS), chemical ionization (CI)) in many Cognac samples followed by grappa, brandy, rum, whisky, vodka, and fruit spirits, and concentrations ranged from traces to 11.2 μg/L. Highest concentrations were obtained in grappa and freshly distilled eaux-de-vie of Cognac samples. Exceeding its detection threshold (100 ng/L, 70 vol %), MND contributes to the anise descriptor of these spirits. Its concentration decreased over aging while being highly correlated with the total amount of fatty acid ethyl ester. In addition, we showed that MND was produced during distillation according to the oxidation state of the white wine as well as the amount of lees used.
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